I know this is a pain, but try it without the massive addon......if you still crash to desktop in the same senarios - then you can rule out the mod......
However - if you don't - it is the mod.....and i hate to say it - the game doesn't crash like that without mods (meaning it will be the mod really).

I took off the massive mod and am using the next generation mod and getting the same problem. it cant be both mods that is doing this.

Yes it could, in fact. I have TNG mod, and I have that same problem (along with some other really annoying bugs). Perhaps it's just mods in general that are causing this?

Just try running Freelancer as is, no mods. If it's still happening, its either a) generic crash bug (game was made by MS, nuff said), or b) a file was modified by FLMM that causes the crash due to it being changed/missing.

FLMM deleted my faction_prop.ini, which in causes my game to crash everytime I load it. This is the second time FLMM has manipulated or deleted a necissary file and caused the game to run improperly. If this is happening, the only thing I've found that works is a complete reinstall.

Delete frelancer (not uninstall), then re-install it. Then use the mods. This makes sure that you have no conflicting files. It could be something in the dll's.

Xeno is correct. Sometimes FLMM will 'leave' by accident a file behind, even though it says deactivation is correct and good. This can then cause you too crash at ANY point in a game (depends what files are missing/changed). So if you delete (not uninstall as this removes MP numbers and other stuff) then just reinstall you will have a 'clean' copy of the game to work with. Also - even though claims are made about how stable the games are, Modded SP games sometimes crash. There is no real knowledge of why - but i have trouble with Hokkaido in SP, being that it crashes in SP all the time when i enter that system (specially round specific points). Why? Something to do with either not supposed to be there, or the fact that i am using an 'open' mod which removes the storyline.